Ontology meeting 2020-01-27: Difference between revisions

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**'results in division of' (GOREL:0001019)
**'results in division of' (GOREL:0001019)
***Not used in the ontology
***Not used in the ontology
***For annotation, it looks like curators primarily used 'occurs in', 'has participant, 'results in division of' although there aren't many annotations at all
****In the ontology, logical definitions use 'occurs in', e.g. cystoblast division = cell division and 'occurs in' some cystoblast
***For annotation, it looks like curators primarily used 'occurs in', 'has participant, 'results in division of' although there aren't many annotation extensions at all for 'cell division' and children
 


*GO
*GO

Revision as of 12:13, 23 January 2020

Conference Line

See calendar for details

On call:

Agenda

Discussion topics

Aligning Ontology, Annotation, ShEx

  • We are creating ontology term-specific shapes in the ShEx schema
  • The goal is to align what is used for annotation with the equivalent expression in logical definitions of the ontology
  • We are also moving towards only using RO relations in GO, i.e. retiring, or incorporating into RO, GOREL relations or RO-pending relations
  • GOREL relations proposed to RO:
  • GOREL relations that could be retired and replaced with an existing RO relation:
    • 'results in division of' (GOREL:0001019)
      • Not used in the ontology
        • In the ontology, logical definitions use 'occurs in', e.g. cystoblast division = cell division and 'occurs in' some cystoblast
      • For annotation, it looks like curators primarily used 'occurs in', 'has participant, 'results in division of' although there aren't many annotation extensions at all for 'cell division' and children


  • GO
 [Typedef]
 id: results_in_division_of
 name: results_in_division_of
 namespace: external
 comment: use occurs_in
 xref: GOREL:0001019
 is_a: has_participant ! has participant
  • GOREL
[Typedef]
id: results_in_division_of
name: results_in_division_of
namespace: go/extensions/gorel
def: "The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type." [GOC:mtg_berkeley_2013]
comment: Example of use: an annotation of gene X to cell division with results_in_division_of CL:0000057 (fibroblast) means that at the end of the process a single fibroblast has divided into two fibroblasts.
subset: AE_cell_or_anatomical
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001019
property_value: local_domain BFO:0000015 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: usage "The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type." xsd:string
domain: BFO:0000015
range: CL:0000000
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: has_participant ! has participant


  • regulates_o_results_in_division_of
    • Not used in the ontology
    • For annotation, it looks like curators primarily used 'regulates o has participant', 'regulates o results in division of' although there are very few of these annotations
[Typedef]
id: regulates_o_results_in_division_of
name: regulates division of
namespace: go/extensions/gorel
def: "This is the combination of the regulates relation with the results_in_division_of relation." [GOC:mtg_berkeley_2013]
subset: display_for_curators
subset: valid_for_annotation_extension
xref: GOREL:0001024
property_value: local_domain GO:0008150 xsd:string
property_value: local_range "CL:0000000 WBbt:0004017" xsd:string
property_value: usage "This is the combination of the regulates relation with the results_in_division_of relation." xsd:string
domain: BFO:0000015
is_a: go_annotation_extension_relation ! go annotation extension relation
is_a: regulates_o_has_participant ! regulates_o_has_participant
equivalent_to_chain: regulates results_in_division_of ! results_in_division_of
  • PROPOSAL: use 'occurs in' for logical definitions and to provide context in annotation for what cell is dividing and 'regulates o occurs in' for standard regulation annotations

Other Business

https://github.com/geneontology/go-ontology/projects/1

Minutes should be recorded on individual tickets and in individual projects